In case anyone cares, I’m still slowly1 working on making a non-beta version of XPlasMap. (The present release is 0.96 [see comments here], so it’s getting incrementally closer to 1.0.) I’ve squashed a few bugs, and added a few features, but much of what I’ve been doing has been kind of shuffling things behind to scenes to make it a little easier to maintain, and also to prepare for adding a couple of features that would have stepped on the toes of the original setup.

I spent the morning trying to figure out why printing was suddenly low-resolution, a bug I thought I had fixed several iterations ago. Turns out the fix only works with the most recent versions of wxPython, whereas I was still working with the builtin 2.8.4.0 in the hope of making the file more portable on Leopard. There’s nothing in the release notes that I can see, but when I switched back to 2.8.7.1 print resolution was back to the proper level again.

There are a couple of things in the ToDos that probably won’t make it into v. 1.0, but most of them should, I think.

XPlasMap ToDos for v 1.0

BUG – Clicking on anything often selects the plasmid rather than the feature itself. (Take the plasmid out of the pathlist)

BUG – Changing gene text parameters overrides text position

BUG – Fix highlights in Cut Dialog

BUG – Split MCS doesn’t work with no downstream sequence/site

BUG – Hide/show text in List View is really slow for a batch of genes!

XPlasMap is lower priority than writing grants, teaching, doing lab work, and taking kids to birthday parties and tobogganing, so that leaves about an hour twice a week, late at night when the kids are asleep, for XPlasMap.[↩]

is there an easy way for me to quickly edit my ApE files to view them in your program?

At the moment the short answer is “No”; sorry. I have had several requests for this and it’s on the list of things to do, but probably not for the next release.

One approach is that ApE exports to GenBank format, as I recall, and XPlasMap will import from GenBank. The bad news is that ApE’s GenBank export doesn’t quite fit the technical standard, and XPlasMap’s GenBank import only follows the strict standard, so it doesn’t recognize ApE’s files. I have written a more forgiving GenBank importer for the next version, so that may help some.

Note: As you suggest correct spacing is essential – for those reading this board you will need to mimic the spacing you find in any genbank file you download from Entrez, which you have NEVER opened in ApE. Do not paste it in as you see it above.

Right, it’s been a couple months since I looked at ApE files but I think the LOCUS line had a couple of places where the spacing was off by one.

Even though it’s not technically correct, though, I think that’s the sort of thing a reasonable parser should be willing to forgive. ApE isn’t the only program to make that sort of mistake (or perhaps they’re working from an older technical spec), I’ve run into it in a couple of other places, so I do want to make importing from GenBank format more generous. (I have a rough version of it working now, but it’s pretty crude and misses a lot of features.)